Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography

• DOI: 10.1002/pmic.202300100
• Publication Date: 2023-06-08T05:25:59Z
• Authors: Lukasz Szyrwiel; Christoph Gille; Michael Mülleder; Vadim Demichev; Markus Ralser
• Keywords: Proteome; False Discovery Rate; Biomarker Discovery

Abstract Increased throughput in proteomic experiments can improve accessibility of platforms, reduce costs, and facilitate new approaches systems biology biomedical research. Here we propose combination analytical flow rate chromatography with ion mobility separation peptide ions, data‐independent acquisition, data analysis the DIA‐NN software suite, to achieve high‐quality from limited sample amounts, at a up 400 samples per day. For instance, when benchmarking our workflow using 500‐μL/min 3‐min chromatographic gradients, report quantification 5211 proteins 2 μg mammalian cell‐line standard high quantitative accuracy precision. We further used this platform analyze blood plasma cohort COVID‐19 inpatients, gradient alternating column regeneration on dual pump system. The method delivered comprehensive view proteome, allowing classification patients according disease severity revealing biomarker candidates.